Who is Participating?

I think it depends on what your last project was, and what you want to emphasize as your strengths. Personally, I rarely find that technical barriers become the most difficult to get past. Most often, it is dealing with the unexpected that makes things difficult. Or working with other people. Adapting with the problem and working with others who may not share your point of view is generally the trickiest thing in my opinion.

To me, saying that learning any application was toughest, will give a negative tone. Interviewer might think that you are week in learning applications.

May be you could just say that extracting low level domain related rules from the legacy application in the absence of any reference/manual/domain personnel was the toughest part of job. From interviewer perspective, this would further minimize chances of extracting negatives.